AMBER Archive (2003)

Subject: Re: problem with tleap

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 08 2003 - 11:12:34 CDT

On Tue, Apr 08, 2003, S.Swaminathan wrote:

> FATAL: Atom .R<PRO 2>.A<HB1 15> does not have a type.

proline should not have an HB1 atom; take a look at the residue libraries.
Since you are just starting out, I recommend letting LEaP add the protons
for you...it will get the names right.

> how do i create libraries for new residues for eg. HEM?

See the $AMBERHOME/dat/contrib directory, or Richard Bryce's web page (link
is on the amber web page.)

> B.the number indicated in case of :
>
> FATAL: Atom .R<HEM 10479>.A<FE 1> does not have a type
>
> is 10479, but in reality, there is no such residue number in the
> atom file.

LEaP adds 10000 to residues in subsequent chains, in order to obtain unique
residue numbers.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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